Proposed European policy in the agricultural sector will place higher emphasis on soil organic carbon (SOC), both as an indicator of soil quality and as a means to offset CO2 emissions through soil carbon (C) sequestration. Despite detailed national SOC data sets in several European Union (EU) Member States, a consistent C stock estimation at EU scale remains problematic. Data are often not directly comparable, different methods have been used to obtain values (e.g. sampling, laboratory analysis) and access may be restricted. Therefore, any evolution of EU policies on C accounting and sequestration may be constrained by a lack of an accurate SOC estimation and the availability of tools to carry out scenario analysis, especially for agricultural soils. In this context, a comprehensive model platform was established at a pan-European scale (EU + Serbia, Bosnia and Herzegovina, Croatia, Montenegro, Albania, Former Yugoslav Republic of Macedonia and Norway) using the agro-ecosystem SOC model CENTURY. Almost 164 000 combinations of soil-climate-land use were computed, including the main arable crops, orchards and pasture. The model was implemented with the main management practices (e.g. irrigation, mineral and organic fertilization, tillage) derived from official statistics. The model results were tested against inventories from the European Environment and Observation Network (EIONET) and approximately 20 000 soil samples from the 2009 LUCAS survey, a monitoring project aiming at producing the first coherent, comprehensive and harmonized top-soil data set of the EU based on harmonized sampling and analytical methods. The CENTURY model estimation of the current 0–30 cm SOC stock of agricultural soils was 17.63 Gt; the model uncertainty estimation was below 36% in half of the NUTS2 regions considered. The model predicted an overall increase of this pool according to different climate-emission scenarios up to 2100, with C loss in the south and east of the area (involving 30% of the whole simulated agricultural land) compensated by a gain in central and northern regions. Generally, higher soil respiration was offset by higher C input as a consequence of increased CO2 atmospheric concentration and favourable crop growing conditions, especially in northern Europe. Considering the importance of SOC in future EU policies, this platform of simulation appears to be a very promising tool to orient future policymaking decisions.